7jvb

X-ray diffraction
3.29Å resolution

Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20

Released:
Model geometry
Fit model/data

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-209784 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spike protein S1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 224 amino acids
Theoretical weight: 25.18 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Nanobody Nb20 Chains: C, D
Molecule details ›
Chains: C, D
Length: 117 amino acids
Theoretical weight: 12.55 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P41212
Unit cell:
a: 70.716Å b: 70.716Å c: 435.037Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.283 0.281 0.322
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21